Officials gave no details of his condition but Mr Navalny's spokeswoman said he had had an allergic reaction with severe facial swelling - something she said he had not experienced before.
A hospital source told Russian media his condition was satisfactory,
An eye doctor who treated Mr Navalny previously is concerned he may have been injured by a chemical substance.
Mr Navalny was jailed for 30 days last week after calling for unauthorised protests, which took place on Saturday.
More than 1,000 people were detained during demonstrations against the barring of opposition candidates in forthcoming local elections.
Mr Navalny's spokeswoman, Kira Yarmysh, tweeted that the opposition leader had never experienced an allergic reaction before.
He was being given the "necessary medical assistance" in a hospital ward under police protection, she said after his transfer to the hospital.
An ophthalmologist who treated him previously says she and a colleague were turned away by the hospital when they tried to see Mr Navalny.
However, Anastasy Vasilyeva adds that, based on what she could see of his face through a door, she cannot exclude the possibility that he might have been injured by a chemical substance.